BIOL1020

How many compounds occur in nature

92

How many compounds are necessary for life + what are the 4 that make up 96%

about 25 are essential to life 

• Carbon, hydrogen, oxygen and nitrogen make up 96% of living matter (CHON)

What is the basic structure of an atom

Each element consists of unique atoms composed of subatomic particles including

• Protons 

• Neutrons

• Electrons

Neutrons and protons form the atomic nucleus

• Electrons form a negatively charged fast moving cloud around the nucleus

• Electrons within atoms are distributed in electron shells, which determine the chemical nature and reactivity of an atom

What is matter

Anything that takes up space and has mass

What is a compound

A substance consisting of 2+ elements in a fixed ratio (eg sodium+chloride=sodium chloride)

What is an isotope

Variant of an element with more neutrons

What are chemical reactions

The making & breaking of chemical bonds leading to changes in the composition of matter are chemical reactions

How do you find atomic number and mass?

All atoms of a particular element have the same number of protons in their nuclei

• the number of protons is the atomic number and is written as a subscript to the left of the symbol for that element.

• unless otherwise indicated an atom is neutral in its electric charge (equal amount of proton

  

  s and electrons)

What are daltons?

• for atoms, subatomic particles and molecules, daltons are used as the unit of measurement

  • Same as atomic mass unit = amu= dalton

  • Neutrons and protons are both 1 dalton

  • Mass of electron is 1/2000th; ignored when computing atom mass

Carbon naturally occuring isotopes

• carbon (atomic number 6) has 3 naturally occurring isotopes

  • carbon 12 (12/6) -99%-

  • carbon-13 (13/6) 

  • and carbon-14 (14/6)

Isotope impact on chemcial reactions

though isotopes of an element have slightly different masses, they behave identically in chemical reactions

How do naturaly occuring isotopes affect atomic mass

• For an element with more than one naturally occurring isotope, the atomic mass is an average of those isotopes, weighted by their abundance.

  • Thus, carbon has an atomic mass of 12.01 daltons.

What are radioactive isotopes

Radioactive isotope: isotope where nucleus decays spontaneously, giving off particles and energy

• when radioactivity decay leads to a change in the number of protons, in transforms the atom to an atom of a different element

EG

• both C12/13 are stable

  • nuclei do not have a tendency to lose subatomic particles

• C-14 is unstable (radioactive)

  • when it decays, a neutron decays into a proton transforming the atom into a nitrogen atom

What are valence electrons

• electrons in outermost shell ‘valence shell’ ; chemical behaviour of an atom is most determined by valence electrons

What happens when a valence shell is completed

• atoms with completed valence shells are unreactive (will not interact readily with other atoms) 

  • Chemically inert

Where are electrons found?

The space where electron is found 90% of time is called an orbital

Electron orbitals: how are they shaped

•  think of an orbital as a component of an electron shell

  • first shell has one spherical s orbital (1s), 

  • second shell has four orbitals (one large spherical orbital (2s) and three dumbbell shaped p orbitals (2p)

What are covalent bonds

• sharing of a pair of valence electrons by 2 atoms

  • eg two hydrogen atoms approach each other (each one has 1 electron but space for 2 in its valence)

  • 1s orbitals overlap

  • they are now both associated with 2 electrons→ covalent bond

  • creates a molecule (in this case hydrogen molecule)

•  each atom that can share valencies has a bonding capacity corresponding to the number of covalent bonds the atom can form

• when bonds form they give the atom a full complement of electrons

Ways of representing molecules: molecular formula

• H₂0

• Subscript indicates the molecule consist of 2 atoms of hydrogen (H) and 1 oxygen

Ways of representing molecules: electron distribution diagram

Ways of representing molecules: lewis dot structure

• shows electron sharing where element symbols are surrounded by dots that represent the valence electrons

• (H : H)

Ways of representing molecules: structural formula

• uses lines to show bonds; single or double depending on type of bond

Ways of representing molecules: space filling models

Uses 3d spheres

What is electronegativity

• Atoms in a molecule attract shared bonding electrons to varying degrees depending on the element

• attraction of a particular atom for the electrons of a covalent bond is called electronegativity

  • the more electronegative, the more strongly it pulls shared electrons to itself

Electronegativity in bonds of the same element

• In a bond between 2 of the same elements, electrons are shared equally as both atoms have the same electronegativity

  • where this happens, the bond is a non-polar covalent bond

    • eg H₂

Electronegativity in bonds of different elements

• When an atom is bonded with a more electronegative atom, the electrons are not shared equally

  • polar  covalent bond

  • eg H₂O

What is ionic bonding

• Two atoms may be so unequal in attraction for valence electrons that the more electronegative atom strips an electron away from its partner

  • results in charged atoms/molecules; ‘ions’

  • The term ion applies to entire molecules that are electrically charged

• the attraction of a cation to an anion forms a 3d lattice/bond

Which ion has what charge, and what happens between them?

• Cation: positively charged

• Anion: negatively charged

How are ionic bonds structured

• unlike covalent compounds, which consist of molecules having definite size/numbers of atoms, ionic compounds do not consist of molecules

  • ionic compounds are rather a ratio of elements in a crystal of the salt (NaCl is not a molecule)

What are hydrogen bonds

• When a hydrogen atom is covalently bonded to an electronegative atom the hydrogen atom has a positive charge

•  This allows it to be attached to a different electronegative atom with a partial negative charge nearby

What are van der waals interactions

• Molecules with non polar covalent bonds may have positive and negatively charged regions

• electrons are not always evenly distributed, hence may accumulate in one part of a molecule or another

• results in ever changing regions of positive and negative charges that enable all atoms and molecules to stick to one another

• individually weak and only occur when atoms and molecules are very close together

How are molecules shaped when consisting of 2 atoms

• molecules consisting of two atoms is always linear

  • Eg H₂ and O₂

What is molecular shape determined by

• most molecules with more than 2 atoms have complicated shapes

• shapes are determined by positions of atoms orbitals

• when an atom forms covalent bonds, orbitals in its valence shell undergo rearrangement

  •  atoms with electrons in s and p orbitals form four new hybrid orbitals shaped like identical teardrops extending from the region of the nucleus

Why is molecular shape important

• determines how biological molecules recognise and respond to one another with specificity

• molecules often bind together temporarily with weak interactions but only if shapes are complementary

• for example opiates have a similar chemical structure to endorphins and are recognised as such by the body

How to write a chemical reaction

• when writing the equation for a chemical reaction use an arrow to indicate the conversion of starting materials (reactants) to resulting materials (products)

• coefficients indicate the number of molecules involved

• all atoms of reactants must be accounted for in the products

Factors affecting reactions

• concentration of reactant

  •  the greater the concentration of reactants, the more frequently they collide with one another to react and form products

  •  as products accumulate, collisions resulting in the reverse reaction become more frequent

  • eventually forward and reverse reactions occur at the same rate as relative frequency of reactants/products stop changing

• called chemical equilibrium where reactions offset each other exactly

• reactions still go off in both directions but with no net effect on concentrations of reactants and pollutants

Structure of water

Wide V with 2 hydrogen atoms joined to the oxygen atom by single covalent bonds\

• Oxygen is more electronegative than hydrogen→ electrons in a covalent bond spend more time closer to the oxygen than hydrogen

• Properties of water come from attractions between oppositely charged atoms of different water molecules

• Partially positive part of water is attracted to partly negative of nearby molecules

  • 2 molecules are held together by a hydrogen bond 

  • when in liquid form, bonds are very fragile (1/20th of a covalent bond)

  • Bonds break and reform with great frequency

• At any given moment, most water molecules are hydrogen bonded to neighbours

Properties of water that make it essential fro. life

1. cohesion

2. moderation of temperature

3. Ice floating on liquid water

What is specific heat

• The specific heat of a substance is the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1c

WHat is waters actual specific heat

• the specific heat of water is therefore 1 calorie per gram and per degree celcius 

What is the significance of waters high specific heat

• compared with most other substances, water has high specific heat

• because of this, water will change its temperature less than other liquids when it absorbs or loses a given amount of heat

Why does water have high specific heat

A) Hydrogen bonding

• heat must be absorbed in order to break hydrogen bonds

• heat is released when hydrogen bonds form

• a calorie of heat causes a relatively small change in the temp of water because much of the heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster

• when the temperature of water drops slightly, many additional hydrogen bonds form releasing a considerable amount of energy in the form of heat

Why his high specific heat importannt for life

• a large body of water can absorb and store a huge amount of heat from the sun in daytime and during summer while warming up only a few degrees

• at night/during winter the gradually cooling water warms the air

• moderates air temperatures in coastal areas

• stabilises ocean temperatures creating favourable environment for marine life

• organisms consist of mostly water- able to resist changes in their own temperature

What is evaporative cooling

• Molecules of any liquid stay close as they are attracted to one another

• Molecules moving fast enough overcome these attractions and depart the liquid to enter the air as gas (vapor)

  • vaporisation/evaporation

• Even at low temperatures some molecules escape into the air

  • Occurs at any temperature

  • If liquid is heated, average kinetic energy of molecules increases→ moves more quickly

What is heat of vaporisation + is it high for water?

• quantity of heat a liquid must absorb for 1g to be converted from liquid to gas states

• same reasons as high specific heat, water has high heat of vaporisation

What is the significance of water’s high heat of vaporisation

• moderates earth's climate; considerable amount of solar heat absorbed by tropical seas is consumed by evaporation of surface water

• as moist tropical air circulates towards poles, it releases heat as it condenses and forms rain

• as liquid evaporates, the surface of the liquid that remains behind cools down (evaporative cooling)

• occurs because liquid that evaporates tends to be the hottest molecules

  •  meaning that as they depart the average heat flattens

What happens to water for temperatures above 4 degrees

• At temperatures above 4 degrees celsius water behaves like other liquids, expanding as it warms and contracting as it cools.

What happens to water below 4 degrees

• As water temperature falls from 4 to 0, water begins to freeze as more and more molecules move too slowly to break hydrogen bonds

WHy does ice float on water

• at 0 degrees, molecules form a crystalline lattice where each water molecule's hydrogen bonds to 4 partners

  • hydrogen bonds keep molecules apart far enough that ice is 10% less dense than liquid water at 4%

• hence ice floats as there is less molecules in the same volume

Why is it important that ice floats

• if ice sank, eventually all water bodies could freeze solid, making life impossible;

  •  during summer only the upper few inches of the ocean would thaw

• instead when a deep body of water cools, the ice floats which insulates liquid water below

• prevents it from freezing, hence allowing life to exist under a frozen surface

What is a solution

• A liquid that is a completely homogenous mixture of substances is a solution

  • dissolving agent is the solvent

• aqueous solution is a solution where water is a solvent

Why is water a solvent

• water is a versatile solvent due to the polarity of the water molecule

  • if a spoonful of salt (NaCl) was placed in water, at the surface of each crystal of salt, sodium and chloride ios are exposed to the solvent

• ions and regions of water molecules are attracted to each other due to their opposite charges

  • oxygens of water have partial negative charges that are attracted to sodium cations

  • hydrogen regions are partially positively charged and are attracted to chlorine anions

• consequently water molecules surrounding the sodium and chloride ions separate and shield them from one another

  • sphere of water molecules is a hydration shell

Does a compound need to be ionic to dissolve in water

• a compound does not need to be ionic to dissolve in water- many compounds are made up of nonionic polar molecules

• such compounds dissolve when water molecules surround each of the solute molecules, forming hydrogen bonds with them

•  proteins can even be dissolved  if they have ionic and polar regions on their surface

What causes hydrophobia

• substances can be hydrophilic without dissolving

  • eg cotton which consists of giant molecules of cellulose, which form hydrogen bonds with water

  • water adheres to cellulose fibres

• hydrophobic substances are those that are nonionic and nonpolar

  • repels water

    • eg vegetable oil; high number of relatively nonpolar covalent bonds

How to determine mass off a molecule

• substances can be hydrophilic without dissolving

  • eg cotton which consists of giant molecules of cellulose, which form hydrogen bonds with water

  • water adheres to cellulose fibres

• hydrophobic substances are those that are nonionic and nonpolar

  • repels water

    • eg vegetable oil; high number of relatively nonpolar covalent bonds

What are mols

• As small numbers cannot be weighed out, we usually measure substances in moles

• A mol represents an exact number of objects 

  • 6.02 x 10²³ (avogadro’s number)

  • There are 6.02 x 10²³  daltons in 1g

• once you determine the molecular mass of a molecule, you use the same number but with the unit gram to represent the mass of 6.02x10^23 molecules of sucrose or 1 mol of sucrose (molar mass)

• to obtain 1 mol of sucrose in the lab, weigh out 342 g

What is the advantage of using mols

Advantage of mols

• a mol of one substance has exactly the same number of molecules as a mole of any other substance

• molarity: number of moles of solute per litre of a solution is the unit most used for aqueous solutions

How are hydroxide ions formed

• Occasionally a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other

  • leaves its electron behind and what is transferred is a hydrogen ion (H+) (a single proton with a 1+ charge)

• The water molecule that lost a proton is now a hydroxide ion (OH-) which has a charge of 1-

• the proton binds to the other water molecule making that molecule a hydronium ion

What is an acid

• A substance that increases the hydrogen ion concentration of a solution

  • Eg eg Hydrochloric acid (HCl): when added to water causes hydrogen ions to dissociate from chloride ions

What are bases

• substance that reduces hydrogen ion concentration of a solution

• some bases reduce H+ concentration directly by accepting hydrogen ions

  • eg ammonia NH₃ acts as a base when a shared electron pair in a nitrogen valence shell attracts a hydrogen ion from the solution

  • resulting in an ammonium ion (NH₄+)

• other bases reduce the H+ concentration indirectly by dissociating to form hydroxide ions which combine with hydrogen ions and form water

  • eg NaOH which in water dissociates into its ions Na+ and OH-

What is the pH scale

• in any aqueous solution at 25 degrees, the product of the H+ and OH- concentrations is constant at 10^-14

• an acid not only adds hydrogen ions to a solution, but also removes hydroxide ions due to the tendency of H+ to combine with OH- forming water

• base has opposite effect

pH=-log[H+]

What are buffers

The internal pH of most living cells is close to 7

• A buffer is a substance that minimises changes in concentrations of H+ and OH- in a solution. 

  • does this by accepting hydrogen ions from the solution when there are in excess and donating hydrogen ions to the solution when they have been depleted

• most buffer solutions contain a weak acid and its corresponding base, which combine reversibly with hydrogen ions

Carbon structure

Carbon has 6 electrons, with 2 in the first electron shell and 4 in the second shell

• Hence, it has 4 electrons in a shell that can hold 8 electrons

• Carbon usually forms single or double covalent bonds

  • when carbon forms 4 bonds, the arrangement of its four hybrid orbitals causes the bonds to angle towards the corners of an imaginary tetrahedron

Significance of carbon electron configuration

• gives covalent compatibility with many different elements

  • In carbon dioxide, a single carbon atom is joined to two atoms of oxygen by double covalent bonds (O=C=O)

  • each line in a structural formula represents a pair of shared electrons

  • thus the two double bonds in CO2 have the same number of shared electrons as 4 single bonds and the arrangement completes the valence shells of all atoms in the molecule

  • As CO₂ is a simple molecule lacking hydrogen, it is often called inorganic despite containing carbon

    • Only has one carbon atom

      • But a carbon atom can also use other electrons to form covalent bonds to other atoms, linking atoms to chains

What are the chemical groups most important in life

HCCASPM

Hydroxyl group (-OH, HO-)

Carbonyl group (>C=O)

Carboxyl group (-COOH)

Amino group (-NH₂) -N<_H^H

Sulfhydryl group(-SH, HS-)

Phosphate group  -OPO₃2-

Methyl group -CH₃

Hydroxyl group

Hydroxyl group (-OH, HO-) Polar due to electronegative oxygen. Forms hydrogen bonds with water, helping to dissolve compounds such as sugars Compound name: alcohol (specific name usually ends in -ol

Carbonyl group

Carbonyl group (>C=O)

Sugars with ketone groups are ketosis. Those with aldehydes are called aldoses. Compound name: Ketone (carbonyl group is within a carbon skeleton) or aldehyde (carbon group is at the end of a carbon skeleton

Corboxyl group

Carboxyl group (-COOH)

Acts as an acid (can donate H+) because the covalent bond between oxygen and hydrogen is so polar Compound name: carboxylic acid/organic acid

Amino group

Amino group (-NH2) -N<HH

Acts as a base. Can pick up an H+ from the surrounding solution (water, in living organisms) Compound name: Amine

Sulfhydryl group

Sulfhydryl group(-SH, HS-)

Two -SH groups can react, forming a cross-link that helsp stabilise protein structure. Hair protein cross-links maintain hair texture. In salons, permanent treatments break cross links then reform in desired shapes Compound name: Thiol

Phosphate group

Phosphate group  -OPO32-

Contributes negative charge (1- when positioned inside a chain of phosphates; 2- when at the end). When attached, confers on a molecule the ability to react with water, releasing energy Compound name: organic phosphate

Methyl group

Methyl group -CH3

Affects the expression of genes when bonded to DNA or to proteins that bind to DNA. Affects the shape and function of male and female sex hormones Compound name: Methylated compound

What is ATP

ATP consists of an organic molecule called adenosine attached to a string of 3 phosphate groups

• where 3 phosphates are present series (such as with atp) one may split off and react with water

•  having lost one phosphate ATP becomes adenine diphosphate (ADP)

• stores the potential to react with water/other molecules→ process that results in the release of energy

What are macromolecules

Large chain-like molecules called polymers. Large carbohydrates, proteins and nucleic acid are macromolecules

What are polymers

long molecule consisting of many similar or identical building blocks linked by covalent bonds. Repeating units that serve as the building blocks of a polymer are smaller molecules called monomers

How are polymers synthesised

• In cells, these processes are facilitated by enzymes

  • Specialised macromolecules (usually proteins) that speed up chemical reactions

• The reaction that connects a monomer to another monomer or polymer is a condensation reaction

  • Reaction in which two molecules are covalently bonded to each with the loss of a small molecule.

What is a dehydration reaction

• Reaction in which two molecules are covalently bonded to each with the loss of a small molecule.

• If a water molecule is lost it is a dehydration reaction

  • Carbohydrate and protein polymers are synthesised by dehydration reactions

  • Each reactant contributes part of the water molecule released during the reaction

  • One provides a hydroxyl gorip (-OH) and the other a hydrogen (-H) this reaction is repeated as monomers are added to the chain one by one, lengthening the poly

    

    mer

How are polymers broken down

• Polymers are disassembled to monomers by hydrolysis

  • Reverse of dehydration reaction

• Bond between monomers is broken by the addition of a water molecule with a hydrogen from water attaching to one monomer and the hydroxyl group attaching to the other

• Eg digestion, where various enzymes attack polymers in digestive tract, speeding up hydrolysis x

What are carbohydrates and what is their purpose

Carbs serve as fuel and building material.

• Carbs include sugars and polymers of sugars

Whar are carb macromolecules

• Carbohydrate macromolecules are polymers called polysaccharides, composed of many sugar building blocks

What are the simplest carbs

• Simplest of carbs are monosaccharides or simple sugars

  • Monomers from which more complex carbohydrates are built

  • Disaccharides are double sugars consisting of two monosaccharides joined by a covalent bond

What are monosaccharides

Monosaccharides generally have molecular formulas that are some multiple of the unit CH₂O. 

• Glucose (C₆H₁₂O₆) is the most common mono saccharide and is of central importance in chemistry of life

• Glucose has qualities of monosaccharide; carbonyl group, multiple hydroxyl groups

• Another criteria for monosaccharides is the size of the carbon skeleton which may be 3-7 carbons long 

Types of monosaccharides

• Depending on the location of the carbonyl group, a monosaccharide is either an aldose (aldehyde sugar) or ketose (ketone sugar)

  • Glucose is an aldose

  • Fructose is an isomer of glucose and is a ketose

Monosaccharide uses

• Monosaccharides, particularly glucose, are major nutrients for cells

  • In cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions

• Carbon skeletons also serve as raw material for the synthesis pf other types of small organic molecules such as amino acids and fatty acids

What is a glycosidic linakge

• Covalent bond formed between to monosaccharides by a dehydration reaction

What are Disaccharides

• Consists of 2 monosacs joined by a glycosidic linkage

• Disaccharides must be broken into monosaccharides to be used for energy by organisms

What are polysaccharides

Macromolecules with a few hundred to a few hundred thousand monosaccharides joined by glycosidic linkages

• Some polysaccharides serve as storage material, hydrolysed as needed to provide monosaccharides for cells

• Others serve as building material for structures that protect the cell or the whole organism

What are storage polysachharides

Long chains of glucose that act as energy resevres

• Starch — the main energy storage polysaccharide in plants.

• Glycogen — the main energy storage polysaccharide in animals and fungi

What are structural polysaccharides

Structural polysaccharides are carbohydrates used for building and supporting biological structures

• cellulose: structures plant walls

• chitin: forms insect exoskeletons

What are lipids

A diverse group of hydrophobic molecules

• Based on molecular structure

  • may have some polar bonds associated with oxygen, but consist mostly of hydrocarbon regions with relatively non polar C-H bonds

Most important lipid types

• fats

• steroids

• phospholipids

What are fats

Fats (also called triglycerides) are made of:

• 1 glycerol molecule

• 3 fatty acid molecules

The fatty acids are attached to glycerol by ester bonds. (formed by condensation reaction)

How are fats made

• Each fatty acid molecule is joined to glycerol by a dehydration reaction

  • Results in am ester linkage 

    • a bond between hydroxyl group and carboxyl group

• Completed fat consists of 3 fatty acids linked to one glycerol molecule

• Fatty acids in fat can be all the same, or can be of 2-3 different kinds

What is the difference between saturated and unsaturated fats

• the structure of the hydrocarbon chains of the fatty acids

• Saturated: no carbon=carbon double bonds 0 saturated with hydrogen

• Unsaturated: one or more double carbon bonds

What is the purpose of fats

• Main purpose is energy storage

• Hydrocarbon chains of fats are rich in energy; one gram of fat stores more than twice as much energy as a gram of a polysaccharide such as starch

• In humans long term food reserves are stocked in adipose cells

• In addition to storing energy, adipose tissue also cushions vital organs 

What are phospholipids

• Similar in structure to a fat molecule but has only 2 fatty acids attached to glycerol rather than 3

  • The 3rd hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge in the cell

• Two ends of phospholipids have different behaviours with respect to water

  • Hydrocarbon tails are hydrophobic

  • Phosphate group and its attachments form a hydrophilic head

What are the purposes of phospholipids

• Essential for cells as they are the major constituent of cell membranes

• When added to water, they assemble into a bilayer that shields the fatty acid tails from water

• At the surface of a cell, phospholipids are arranged in a similar bilayer, forming a boundary between the cell and its external environment 

• Establishes separate compartments within eukaryotic cells

What are steroids

Lipids characterised by a carbon skeleton consisting of 4 fused rinks

• Different steroids are distinguished by the particular chemical groups attached to the ensemble of rings

  • Eg cholesterol, used in animal cell membranes and as a precursor for other steroids to be synthesised

What are proteins

• Include a diversity of structures, resulting in a wide variety of functions

• Account for 50% of the dry mass of most cells

• Constructed from the same set of 20 amino acids, linked in unbranched polymers

  • Bond between amino acids is a peptide bond, polymer of amino acids is a polypeptide

• Protein is made up of one or more polypeptides, each folded and coiled into a 3d structure

Enzymatic protein function +example

Selective acceleration of chemical reactions

Digestive enzymes catalyse the hydrolysis of bonds in food molecules